After a bit more testing and one full day of evaluation Wikiless is now restored.
The aggressive caching didn't really help. I added Anubis on top of Wikiless and after a few minutes it completely removed the rate limit on the back-end.
Meaning JavaScript is now required for Wikiless but the barrage of bot requests gets filtered out. In my opinion a fair trade off.
Shoutout to Anubis. This software is incredible at stopping bots/scrapers https://github.com/TecharoHQ/anubis